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LOC129995605 ATAC-STARR-seq lymphoblastoid active region 23868 [ Homo sapiens (human) ]

Gene ID: 129995605, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129995605
Gene description
ATAC-STARR-seq lymphoblastoid active region 23868
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence represents an accessible chromatin region that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC129995605 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (1739666..1740005)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (1602815..1603154)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (1739900..1740239)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16824 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23864 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:1613862-1614479 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:1614480-1615096 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:1618844-1619706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23865 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:1629302-1630229 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:1630230-1631156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:1633959-1634459 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:1636810-1637341 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:1644131-1645078 Neighboring gene uncharacterized LOC107986514 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23866 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23867 Neighboring gene forkhead box C1 Neighboring gene GDP-mannose 4,6-dehydratase Neighboring gene NANOG hESC enhancer GRCh37_chr6:1729872-1730373 Neighboring gene uncharacterized LOC124901239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23869 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:1873801-1874302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:1874303-1874803 Neighboring gene NANOG hESC enhancer GRCh37_chr6:1919859-1920404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16825 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:1952649-1953848 Neighboring gene MPRA-validated peak5622 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr6:2117206-2117756 Neighboring gene Sharpr-MPRA regulatory region 5333 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23871 Neighboring gene NANOG hESC enhancer GRCh37_chr6:2222412-2223029 Neighboring gene Sharpr-MPRA regulatory region 10202 Neighboring gene uncharacterized LOC107986512

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_175051.1 

    Range
    101..440
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    1739666..1740005
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    1602815..1603154
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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